Contacts of the strand formed by residues 206 - 211 (chain A) in PDB entry 6F0X


Residue contacts within the protein are derived with the CSU software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332). A short description of the analytical approach is given at the end of the page.
For CSU analysis of other PDB entry

Note:
Non-standard 3 letter residue codes indicate a heterogroup. To identify and analyse, use LPC software

Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB   - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC   - hydrophobic-hydrophilic contact (destabilizing contact)
+/-  - indicates presence/absence of a specific contacts
*    - indicates residues forming contacts  by their side chain
       (including CA atoms)
Residues in contact with TYR 206 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126A  VAL*     5.1    13.5    -      -       +      -
    127A  LEU*     3.8    19.1    -      -       +      -
    128A  PRO*     5.8     2.5    -      -       +      -
    197A  THR*     5.4     1.1    -      -       -      -
    204A  TYR*     4.2     1.3    -      -       -      +
    205A  ARG*     1.3    99.8    -      -       +      +
    207A  GLY*     1.3    71.3    +      -       -      +
    208A  GLN*     5.0    10.3    -      -       +      -
    242A  ASP*     3.8    21.5    +      -       -      -
    244A  ASP*     3.4     4.7    +      -       +      +
    245A  ALA*     2.6    33.8    -      -       +      -
    246A  LEU*     2.9     6.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 207 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126A  VAL*     3.9     0.9    -      -       -      -
    127A  LEU*     3.2    32.6    +      -       -      +
    206A  TYR*     1.3    86.0    -      -       -      +
    208A  GLN*     1.3    74.0    +      -       -      -
    245A  ALA*     3.5    12.6    -      -       -      -
    246A  LEU      3.2    13.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 208 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124A  HIS*     3.0    40.7    +      -       -      +
    125A  TRP      2.8    22.5    +      -       -      +
    126A  VAL*     4.1    13.3    -      -       -      +
    127A  LEU*     4.9     2.7    -      -       -      -
    206A  TYR*     5.0    11.5    -      -       +      -
    207A  GLY*     1.3    85.2    +      -       -      -
    209A  LEU*     1.3    58.6    +      -       -      +
    210A  ILE*     4.1     9.1    -      -       +      +
    239A  LEU*     3.7    39.4    -      -       +      +
    245A  ALA*     5.0     2.2    -      -       +      +
    246A  LEU      3.5     4.5    +      -       -      +
    247A  VAL*     3.9     5.8    -      -       +      +
    248A  PHE*     3.0    31.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 209 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    125A  TRP*     2.9    69.1    +      -       +      +
    127A  LEU*     4.9     9.6    -      -       +      -
    132A  PHE*     5.1     8.1    -      -       +      -
    190A  LYS*     4.4    26.5    -      -       +      +
    193A  ALA*     4.8    13.7    -      -       +      -
    208A  GLN*     1.3    73.9    -      -       -      +
    210A  ILE*     1.3    63.9    +      -       -      +
    248A  PHE*     3.1    35.7    -      -       +      +
    249A  VAL      3.9    12.8    -      -       -      +
    250A  LEU*     4.2    12.6    -      -       +      -
    296A  LEU*     5.2     4.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 210 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    122A  ALA*     5.0     6.1    -      -       +      -
    123A  ASN      3.1    19.1    -      -       -      +
    124A  HIS*     3.6    31.2    -      -       +      -
    125A  TRP*     4.7     0.4    -      -       -      -
    208A  GLN*     4.1    17.5    -      -       +      +
    209A  LEU*     1.3    81.6    -      -       -      +
    211A  GLU*     1.3    71.0    +      -       -      +
    212A  ILE*     3.1    20.4    +      -       +      +
    232A  MET*     5.8     2.7    -      -       +      -
    235A  LYS*     6.5     0.9    -      -       +      -
    236A  ILE*     4.9    18.8    -      -       +      -
    239A  LEU*     4.5    10.3    -      -       +      -
    248A  PHE      3.4    10.7    +      -       -      +
    249A  VAL*     4.4     5.5    -      -       +      -
    250A  LEU*     3.6    19.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 211 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    122A  ALA*     2.6    38.4    -      -       -      +
    123A  ASN*     2.9    37.6    +      -       -      +
    125A  TRP*     3.1    41.3    -      -       +      -
    190A  LYS*     5.9     0.4    -      -       -      -
    210A  ILE*     1.3    70.0    -      -       -      +
    212A  ILE*     1.3    54.1    +      -       -      +
    213A  ASN*     4.2    23.7    +      -       +      +
    250A  LEU*     4.6    12.6    -      -       +      -
    252A  ASP*     6.3     3.4    -      -       +      -
    282B  THR*     5.6     3.3    -      -       -      +
    286B  GLN*     3.0    26.3    +      -       -      -
----------------------------------------------------------
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A short description of the analytical approach
The contact analysis used in this page is based upon the approach developed in: Sobolev V., Wade R.C., Vriend G. and Edelman M. PROTEINS (1996) 25, 120-129. Contact legitimacy depends on the hydrophobic-hydrophilic properties of the contacting atoms. In order to define it, for each inter-atomic contact, eight atom classes have been introduced:


   I  Hydrophilic      - N and O that can donate and accept hydrogen bonds
                         (e.g., oxygen of hydroxyl group of Ser. or Thr)
  II  Acceptor         - N or O that can only accept a hydrogen bond
 III  Donor            - N that can only donate a hydrogen bond
  IV  Hydrophobic      - Cl, Br, I and all C atoms that are not in
                         aromatic rings and do not have a covalent bond to
                         a N or O atom
   V  Aromatic         - C in aromatic rings irrespective of any other 
                         bonds formed by the atom
  VI  Neutral          - C atoms that have a covalent bond to at least one
                         atom of class I or two or more atoms from class II
                         or III; atoms; S, F, P, and metal atoms in all cases
 VII  Neutral-donor    - C atoms that have a covalent bond with only one
                         atom of class III
VIII  Neutral-acceptor - C atoms that have a covalent bond with only 
                         one atom of class II
For each pair of contacts the state of legitimacy is shown below:

Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
  Atomic class           I  II  III   IV   V   VI  VII  VIII
------------------------------------------------------------
   I  (Hydrophilic)      +   +    +    -   +   +    +    +
  II  (Acceptor)         +   -    +    -   +   +    +    -
 III  (Donor)            +   +    -    -   +   +    -    +
  IV  (Hydrophobic)      -   -    -    +   +   +    +    +
   V  (Aromatic)         +   +    +    +   +   +    +    +
  VI  (Neutral)          +   +    +    +   +   +    +    +
 VII  (Neutral-donor)    +   +    -    +   +   +    -    +
VIII  (Neutral-acceptor) +   -    +    +   +   +    +    -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically assigned based on the atomic coordinates. However, in three cases (see below) the automatic assignment is currently ambiguous. In these cases, the user is advised to manually analyse the full list of contacts using LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are 
   considered "aromatic" (Class V) if the ring is approximately
   planar, and "hydrophobic" (Class IV) or "neutral" (Classes
   VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
   "hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
   "carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).

Please E-mail any questions and/or suggestions concerning this page to Vladimir.Sobolev@weizmann.ac.il